The proposed Q Exactive instrument from Thermo Scientific is a robust, high throughput, and high resolution mass spectrometer(1,2) based on high performance quadrupole mass selection and high resolution Orbitrap ion detection. It implements enhanced Fourier transform or eFT(3) algorithm for improved mass resolving power. The proposed Q Exactive instrument has several advantages over our current most powerful LTQ Orbitrap Velos instrument. The scan rate of HCD MSMS is nearly three times higher and the MSMS product ion detection efficiency is also higher. The combined effect allows the instrument to identify more peptides. As demonstrated in our comparison experiments, 2-3X more peptides are identified on the proposed instrument over those on the Velos Orbitrap. The Q Exactive mass spectrometer will help users identify and quantify post-translational modifications (PTM) from complex biological samples, determine protein complex structures, and study protein dynamics using strategically different approaches. A suite of University of California investigators will be major users and be helped in the identification and quantification of post-translational modifications (including site-specific phosphorylation and ubiquitination, fo example), proteolytically cleaved substrate networks (e.g., caspases, granzymes), host-pathogen protein interaction dynamics (HIV, T. bacillus, etc.) and drug inhibitors of kinases in patient cohorts.